Part I: Introductory Materials Introduction to R

1. Part I: Introductory MaterialsIntroduction to R Dr. Nagiza F. Samatova Department of Computer Science North Carolina State University and Computer Science and Mathematics Division Oak Ridge National Laboratory

2. What is R and why do we use it? • Open source, most widely used for statistical analysis and graphics • Extensible via dynamically loadable add-on packages • >1,800 packages on CRAN > v = rnorm(256) > A = as.matrix (v,16,16) > summary(A) > library (fields) > image.plot (A) > … > dyn.load( “foo.so”) > .C( “foobar” ) > dyn.unload( “foo.so” )

3. Why R? • Statistics & Data Mining • Commercial Statistical computing and graphics • Technical computing • Matrix and vector formulations http://www.r-project.org • Developed by R. Gentleman & R. Ihaka • Expanded by community as open source • Statistically rich • Data Visualization and analysis platform • Image processing, vector computing

4. The Programmer’s Dilemma Productivity Performance High- Level Languages Low-Level Languages What programming language to use & why? Assembly Object Oriented (C++, Java) Functional languages (C, Fortran) Scripting (R, MATLAB, IDL)

5. Features of R • R is an integrated suite of software for data manipulation, calculation, and graphical display • Effective data handling • Various operators for calculations on arrays/matrices • Graphical facilities for data analysis • Well-developed language including conditionals, loops, recursive functions and I/O capabilities.

6. Basic usage: arithmetic in R • You can use R as a calculator • Typed expressions will be evaluated and printed out • Main operations: +, -, *, /, ^ • Obeys order of operations • Use parentheses to group expressions • More complex operations appear as functions • sqrt(2) • sin(pi/4), cos(pi/4), tan(pi/4), asin(1), acos(1), atan(1) • exp(1), log(2), log10(10)

7. Getting help • help(function_name) • help(prcomp) • ?function_name • ?prcomp • help.search(“topic”) • ??topic or ??“topic” • Search CRAN • http://www.r-project.org • From R GUI: Help  Search help… • CRAN Task Views (for individual packages) • http://cran.cnr.berkeley.edu/web/views/

8. Variables and assignment • Use variables to store values • Three ways to assign variables • a = 6 • a <- 6 • 6 -> a • Update variables by using the current value in an assignment • x = x + 1 • Naming rules • Can include letters, numbers, ., and _ • Names are case sensitive • Must start with . or a letter

9. R Commands • Commands can be expressions or assignments • Separate by semicolon or new line • Can split across multiple lines • R will change prompt to + if command not finished • Useful commands for variables • ls(): List all stored variables • rm(x): Delete one or more variables • class(x): Describe what type of data a variable stores • save(x,file=“filename”): Store variable(s) to a binary file • load(“filename”): Load all variables from a binary file • Save/load in current directory or My Documents by default

10. Vectors and vector operations To access vector elements: # 2nd element of x x[2] # first five elements of x x[1:5] # all but the 3rd element of x x[-3] # values of x that are < 40 x[x<40] # values of y such that x is < 40 y[x<40] To perform operations: # mathematical operations on vectors y=c(3,2,4,3,7,6,1,1) x+y; 2*y; x*y; x/y; y^2 To create a vector: # c() command to create vector x x=c(12,32,54,33,21,65) # c()to add elements to vector x x=c(x,55,32) # seq() command to create sequence of number years=seq(1990,2003) # to contain in steps of .5 a=seq(3,5,.5) # can use : to step by 1 years=1990:2003; # rep() command to create data that follow a regular pattern b=rep(1,5) c=rep(1:2,4)

11. Matrices & matrix operations To create a matrix: # matrix() command to create matrix A with rows and cols A=matrix(c(54,49,49,41,26,43,49,50,58,71),nrow=5,ncol=2)) B=matrix(1,nrow=4,ncol=4) Statisticaloperations: To access matrix elements: # matrix_name[row_no, col_no] A[2,1]# 2nd row, 1st column element A[3,] # 3rd row A[,2] # 2nd column of the matrix A[2:4,c(3,1)]# submatrix of 2nd-4th elements of the 3rd and 1st columns A["KC",] # access row by name, "KC" rowSums(A) colSums(A) rowMeans(A) colMeans(A) # max of each columns apply(A,2,max) # min of each row apply(A,1,min) Element by elementops: Matrix/vector multiplication: 2*A+3; A+B; A*B; A/B; A %*% B;

12. Useful functions for vectors and matrices • Find # of elements or dimensions • length(v), length(A), dim(A) • Transpose • t(v), t(A) • Matrix inverse • solve(A) • Sort vector values • sort(v) • Statistics • min(), max(), mean(), median(), sum(), sd(),quantile() • Treat matrices as a single vector (same with sort())

13. Graphical display and plotting • Most common plotting function is plot() • plot(x,y) plots yvsx • plot(x) plots xvs1:length(x) • plot() has many options for labels, colors, symbol, size, etc. • Check help with ?plot • Use points(), lines(), or text() to add to an existing plot • Use x11() to start a new output window • Save plots with png(), jpeg(), tiff(), or bmp()

14. R Packages • R functions and datasets are organized into packages • Packages base and stats include many of the built-in functions in R • CRAN provides thousands of packages contributed by R users • Package contents are only available when loaded • Load a package with library(pkgname) • Packages must be installed before they can be loaded • Use library() to see installed packages • Use install.packages(pkgname) and update.packages(pkgname) to install or update a package • Can also run R CMD INSTALL pkgname.tar.gz from command line if you have downloaded package source

15. Exploring the iris data • Load iris data into your R session: • data (iris); • help (data); • Check that iris was indeed loaded: • ls (); • Check the class that the iris object belongs to: • class (iris); • Read Sections 3.4 and 6.3 in “Introduction to R” • Print the content of iris data: • iris; • Check the dimensions of the iris data: • dim (iris); • Check the names of the columns: • names (iris);

16. Exploring the iris data (cont.) • Plot Petal.Length vs. Petal.Width: • plot (iris[ , 3], iris[ , 4]); • example(plot) • Exercise: create a plot similar to this figure: Src: Figure is from Introduction to Data Mining by Pang-Ning Tan, Michael Steinbach, and Vipin Kumar

17. Reading data from files • Large data sets are better loaded through the file input interface in R • Reading a table of data can be done using the read.table() command: • a <- read.table(“a.txt”) • The values are read into R as an object of type data frame (a sort of matrix in which different columns can have different types). Various options can specify reading or discarding of headers and other metadata. • A more primitive but universal file-reading function exists, called scan() • b = scan(“input.dat”); • scan() returns a vector of the data read

18. Programming in R • The following slides assume a basic understanding of programming concepts • For more information, please see chapters 9 and 10 of the R manual: http://cran.r-project.org/doc/manuals/R-intro.html Additional resources • Beginning R: An Introduction to Statistical Programming by Larry Pace • Introduction to R webpage on APSnet: http://www.apsnet.org/edcenter/advanced/topics/ecologyandepidemiologyinr/introductiontor/Pages/default.aspx • The R Inferno: http://www.burns-stat.com/pages/Tutor/R_inferno.pdf

19. Conditional statements • Perform different commands in different situations • if (condition) command_if_true • Can add else command_if_falseto end • Group multiple commands together with braces {} • if (cond1) {cmd1; cmd2;} else if (cond2) {cmd3; cmd4;} • Conditions use relational operators • ==, !=, <, >, <=, >= • Do not confuse = (assignment) with == (equality) • = is a command, == is a question • Combine conditions with and (&&) and or (||) • Use & and | for vectors of length > 1 (element-wise)

20. Loops • Most common type of loop is the for loop • for (x in v) { loop_commands; } • v is a vector, commands repeat for each value in v • Variable x becomes each value in v, in order • Example: adding the numbers 1-10 • total = 0; for (x in 1:10) total = total + x; • Other type of loop is the while loop • while (condition) { loop_commands; } • Condition is identical to if statement • Commands are repeated until condition is false • Might execute commands 0 times if already false • while loops are useful when you don’t know number of iterations

21. Scripting in R • A script is a sequence of R commands that perform some common task • E.g., defining a specific function, performing some analysis routine, etc. • Save R commands in a plain text file • Usually have extension of .R • Run scripts with source() : • source(“filename.R”) • To save command output to a file, use sink(): • sink(“output.Rout”) • sink() restores output to console • Can be used with or outside of a script

22. Lists • Objects containing an ordered collection of objects • Components do not have to be of same type • Use list() to create a list: • a <- list(“hello”,c(4,2,1),“class”); • Components can be named: • a <- list(string1=“hello”,num=c(4,2,1),string2=“class”) • Use [[position#]] or $name to access list elements • E.g., a[[2]] and a$num are equivalent • Running the length() command on a list gives the number of higher-level objects

23. Writing your own functions • Writing functions in R is defined by an assignment like: • a <- function(arg1,arg2) { function_commands; } • Functions are R objects of type “function” • Functions can be written in C/FORTRAN and called via .C() or .Fortran() • Arguments may have default values • Example: my.pow <- function(base, pow = 2) {return base^pow;} • Arguments with default values become optional, should usually appear at end of argument list (though not required) • Arguments are untyped • Allows multipurpose functions that depend on argument type • Use class(), is.numeric(), is.matrix(), etc. to determine type

24. How do I get started with R (Linux)? Step 1: Download R mkdir for RHOME; cd $RHOME wget http://cran.cnr.berkeley.edu/src/base/R-2/R-2.9.1.tar.gz Step 2: Install R tar –zxvf R-2.9.1.tar.g ./configure --prefix=<RHOME> --enable-R-shlib make make install Step 3: Run R Update env. variables in $HOME/.bash_profile: export PATH=<RHOME>/bin:$PATH export R_HOME=<RHOME> R

25. Useful R links R Home:http://www.r-project.org/ R’s CRAN package distribution:http://cran.cnr.berkeley.edu/ Introduction to R manual: http://cran.cnr.berkeley.edu/doc/manuals/R-intro.pdf Writing R extensions:http://cran.cnr.berkeley.edu/doc/manuals/R-exts.pdf Other R documentation: http://cran.cnr.berkeley.edu/manuals.html